Molecular modeling on the recognition of DNA sequence and conformational repair of sheared DNA by novel chiral metal complex D,L-[Co(phen)2hpip]3+

A study on the recognition of DNA sequence and conformational repair of sheared DNA by Novel Chiral Metal complex D,L-[Co(phen)₂hpip]³⁺ (phen=1,10 phenanthroline, hpip=2-[2-hydroxyphenyl] imidazole [4,5-f][1,10] phenanthroline) is carried out with molecular simulations. The results reveal that two isomers of the complex could both recognize the normal DNA in the minor groove orientation, while recognize the sheared DNA in the major groove orientation and both isomers could convert the conformation of mismatched bases from sheared form to parallel form. Further analysis shows that the steric details of complex’s intercalation to base stack determine the results of recognition, which is induced by the steric collision among ancillary ligand phen, bases and DNA backbone, and by the steric crowding occurring in the process of structural expansion of bases and DNA backbone. Detailed analysis reveals that the conformational repair of mismatched bases relates not only to the steric interactions, but also the π-π stack among normal bases, mismatched bases and hpip ligand.     

Molecular modeling on the recognition of DNA sequence and conformational repair of sheared DNA by novel chiral metal complex D,L-[Co(phen)2hpip]3+

A study on the recognition of DNA sequence and conformational repair of sheared DNA by Novel Chiral Metal complex D,L-[Co(phen)₂hpip]³⁺ (phen=1,10 phenanthroline, hpip=2-[2-hydroxyphenyl] imidazole [4,5-f][1,10] phenanthroline) is carried out with molecular simulations. The results reveal that two isomers of the complex could both recognize the normal DNA in the minor groove orientation, while recognize the sheared DNA in the major groove orientation and both isomers could convert the conformation of mismatched bases from sheared form to parallel form. Further analysis shows that the steric details of complex’s intercalation to base stack determine the results of recognition, which is induced by the steric collision among ancillary ligand phen, bases and DNA backbone, and by the steric crowding occurring in the process of structural expansion of bases and DNA backbone. Detailed analysis reveals that the conformational repair of mismatched bases relates not only to the steric interactions, but also the π-π stack among normal bases, mismatched bases and hpip ligand.     

手性配合物Λ, Δ-[Ru(phen)2hpip]2+的两种结构对含G:T错配DNA识别的分子力学研究

In this work, the recognition of DNA including G：T mismatched pairs by the two different structures of [Ru（phen）2hpip]^2＋ was firstly studied with molecular modeling respectively. The results revealed that all of the four chiral isomers of the two structures could recognize the mismatched DNA from the minor groove orientation especially and the interaction was enantioselective and sitespecific. The two left isomers were more preferential than the right ones. Especially, the structure Ⅱ which had much lower energy after interacting with DNA was the advantaged structure. Detailed energy analysis indicated that the steric interaction in the process of the complex inserting base stack determined the recognition results and the electrostatic interaction made an effect to some extent.     

Molecular modeling on recognition of sheared and normal DNA by novel metal complex Λ- and Δ-[Co(phen)2hpip]

Recognition of sheared and normal DNA by a novel metal complex [Co(phen)₂hpip]³⁺ (phen=1,10-phenanthroline, HPIP=2-(2-hydroxyphenyl)imidazole[4,5-f][1,10]phenanethroline) is studied by molecular modeling. Calculating results indicate that, this complex can specifically recognize DNA segment of sequence –MMNNMM– (M means mismatch base pairs and N means normal base pairs). Intercalating from minor groove between the middle normal duplex into the sheared DNA with the depth of 1.2 nm is of preference and enantioselectivity is observed. Comparison on the two DNA structures of optimal conformation and analysis on the interaction between DNA and the two tail ligands of the complex show that, the effect of the two neighboring mismatch duplexes on the structure of the middle normal base pairs and the steric interaction between the mismatch duplexes and the two tail ligands of the complex are the essential reason to the segment specificity. Investigation on the detailed energy terms indicate that, in effecting enantioselectivity, the electrostatic distribution of the complex is in the majority and steric interaction is at the next place. But, steric interaction is surely the only factor determining the intercalating from minor groove.     

铜(Ⅱ)-邻菲咯啉-(邻菲咯啉-5,6-二酮)络合物的合成及其同脱氧核糖核酸的作用

以邻菲咯啉（phen)、邻菲咯啉－5，6－二酮（dione)为配体首次合成了高氯酸邻菲咯啉－邻菲咯啉－5，6－二酮（Ⅱ）。用荧光光谱，摩尔比，粘度，MLCT减色效应，平衡常数以及荧光能量转移研究了各合物与鱼精子DNA的结合情况，证实了该络合物与DNA存在插入作用。基于络合物对DNA能量转移造成荧光量子产率比值（Φλ/Φ320）的降低，解释了不同波长激发光下，荧光发射峰在加入DNA后产生猝灭和增强两种绝然不同的现象。     

The selective recognition of mismatched d(GCGAGC)_2 by the cobalt(III) complex

Base mismatches arise naturally in the life cycleof a cell as a result of either polymerase error or DNAdamage. Under most circumstances the cell correctsthese mispairings using a complex repair system toprevent mutations in the genetic code. Experimental…     

The selective recognition of mismatched d(GCGAGC)2 by the cobalt(III) complex

We studied the binding of [Co(phen)₂(HPIP)]CI₃ to mismatched d(GCGAGC)₂ containing two sheared G:A mispairs by NMR. The result shows that the complex was intercalated into G:A region from the minor groove and extended to the major groove, and could selectively recognize the mispairs.³¹P NMR indicates that the complex binding induced the change of the phosphate backbone in the mismatched base pairs region.     

Red-light photosensitized cleavage of DNA by (l-lysine)(phenanthroline base)copper(II) complexes

Ternary copper(II) complexes [Cu(l-lys)B(ClO4)](ClO4)(1-4), where B is a heterocyclic base, viz. 2,2'-bipyridine (bpy, 1), 1,10-phenanthroline (phen, 2), dipyrido[3,2-d:2',3'-f]quinoxaline (dpq, 3) and dipyrido[3,2-a:2',3'-c]phenazene (dppz, 4), are prepared and their DNA binding and photo-induced DNA cleavage activity studied (l-lys =l-lysine). Complex 2, structurally characterized by X-ray crystallography, shows a square-pyramidal (4 + 1) coordination geometry in which the N,O-donor l-lysine and N,N-donor heterocyclic base bind at the basal plane and the perchlorate ligand is bonded at the elongated axial site. The crystal structure shows the presence of a pendant cationic amine moiety -(CH2)4NH3+ of l-lysine. The one-electron paramagnetic complexes display a d-d band in the range of 598-762 nm in DMF and exhibit cyclic voltammetric response due to Cu(II)/Cu(I) couple in the range of 0.07 to -0.20 V vs. SCE in DMF-Tris-HCl buffer. The complexes having phenanthroline bases display good binding propensity to the calf thymus DNA giving an order: 4 (dppz) > 3 (dpq) > 2 (phen)> 1 (bpy). Control cleavage experiments using pUC19 supercoiled DNA and distamycin suggest major groove binding for the dppz and minor groove binding for the other complexes. Complexes 2-4 show efficient DNA cleavage activity on UV (365 nm) or visible light (694 nm ruby laser) irradiation via a mechanistic pathway involving formation of singlet oxygen as the reactive species. The amino acid l-lysine bound to the metal shows photosensitizing effect at red light, while the heterocyclic bases are primarily DNA groove binders. The dpq and dppz ligands display red light-induced photosensitizing effects in copper-bound form.     

Studies on the Interaction of Dinitratobis（phen） Cadmium Complex with DNA

DNA-binding properties of the dinitratobis（phen） cadmium complex [Cd（phen）2（NO3）2] （where phen = 1,10-phenanthroline） have been investigated with absorption titration, fluorescence spectroscopy, viscosity measurement, molecular modeling and density functional theory （DFT） calculations. The results indictate DNA-binding mode of the complex to be weak groove binding rather than partial intercalative interaction expected of the extended planar aromatic phen ring. In addition, the DNA cleavage study was carried out by gel electrophoresis experiment. The results showed that the complex both hardly cleaves pBR322 DNA in the absence and present ascorbate. So it is suggested that the formation of cadmium complex can decrease cadmium toxicity to some extents.     

Synthesis and spectroscopic DNA binding studies of homoleptic and heteroleptic ruthenium(II) complexes with imidazo[4,5-f] [1,10]phenanthroline or its derivatives

Two series of new complexes, [Ru(phen)2L]2+ and [RuL3]2+, where phen = 1,10-phenanthroline, and L denotes imidazo[4,5-f][1,10]phenanthroline (IP) or 2-(4-R-phenyl)imidazo[4,5-f][1,10]phenanthroline(PIP, R = H; HOP, R = –OH; MOP, R = –OMe; DMNP, R = NMe2; CLP, R = Cl; NOP, R = NO2), were synthesized and characterized. Their binding to calf thymus DNA was investigated using electronic absorption and emission spectroscopy. [Ru(IP)3]2+ and each [Ru(phen)2 L]2+ showed dramatic absorption hypochromism and bathochromicity, as well as steady-state emission intensity and excited-state lifetime enhancements {except nonluminescent [Ru(phen)2NOP]2+} associated with the presence of DNA, inferring that they bind to DNA by intercalation. These phenomena were not observed for [RuL3]2+ type complexes (except L = IP), indicating that they bind to DNA at most through electrostatic interactions.     

△,Λ-[Co(phen)2tpphz]^3+与B - DNA相互作用的分子 模拟

针对国际上对金属配合物同DNA间作用机量的争议,采用分子模拟手段在MM2力场下,搭建并优化了手性金属配合物△,Λ-[Co(phen)2tpphz]^3+与B-DNA[d(GTCGATCGAC)2]的模型,继而对其相互作用进行了模拟,得出的结论是：对所采用的B-DNA片断,该金属配合物有明显的立体选择性△型配合物从小沟插入占明显优势,而且,总体来看,从AT区插入更易进行。     

手性金属配合物Δ,Λ-[Ru(IP)2dppz]2＋对含G:T错配的环丁烷嘧啶二聚体识别和部分构型修复的分子力学研究

环丁烷嘧啶二聚体(Cyclobutane Pyrimidine Dimer, CPD)是紫外线对DNA损伤导致皮肤癌的首要环节, XPC-hHR23B是最早作为对CPD的损伤识别剂的, 但其识别效率很低. 本文首次采用分子力学方法模拟了一种新的手性金属配合物Δ,Λ-[Ru(IP)₂dppz]^2＋对含G:T错配的CPD双螺旋DNA的识别作用. 模拟结果显示: 金属配合物[Ru(IP)₂dppz]^2＋的两个手性异构体都对含G:T错配的CPD双螺旋DNA具有识别作用, 识别的过程体现了很强的手性选择性、沟选择性和位点特异性. 同时, 我们发现: 在Λ-[Ru(IP)₂dppz]^2＋插入到CPD后, 形成CPD的两个T碱基由原来的敞口形状部分地转为近平行状, 使其在构型上得到初步的修复.     

Speciation of ternary cobalt(II) phenanthroline-silica surface complexes as a function of pH and ligand steric bulk

Co(II) solution species containing 1 equiv of phenanthroline (phen), 2-methyl-1,10-phenanthroline (MMP), or 2,9-dimethyl-1,10-phenanthroline (DMP) ligand formed inner-sphere surface complexes when grafted on silica. The speciation on the silica surface depended on both the pH of the grafting solution and the steric bulk of the ligand. [Co(DMP)](2+) formed tetrahedral surface adducts exclusively, with a 1:1 ligand-Co ratio. These surface adducts were first detectable at pH values above 5.1. [Co(MMP)](2+) and [Co(phen)](2+) formed exclusively octahedral adducts on the surface with a 1:1 ligand-Co ratio at pH values below 5. The [Co(MMP)](2+) complex formed a tetrahedral adduct initially at pH 6 and increasingly as the pH was raised. The [Co(phen)](2+) complex did not produce a comparable tetrahedral surface species under any conditions. Instead, mixtures of octahedral surface species with both 1:1 and 2:1 ligand-Co ratios began to form at pH values above 6. Taken together, the results indicated that the development of tetrahedral stereochemistry was strongly influenced by steric factors in the presence of a nitrogen-donating ligand. All three phenanthroline derivatives promoted surface binding of the Co(II) ion adducts, so that maximal binding occurred at lower pH values than for binding of [Co(H(2)O)(6)](2+), which formed exclusively tetrahedral adducts.     

Effect of the Ancillary Ligands on the Spectral Properties and G‐Quadruplexes DNA Binding Behavior: A Combined Experimental and Theoretical Study

In an effort to explore the effect of ancillary ligands on the spectral properties and overall G‐quadruplex DNA binding behavior, two new ruthenium(II) complexes [Ru(phen)₂(dppzi)]²⁺ ( 1 ) and [Ru(dmp)₂(dppzi)]²⁺ ( 2 ) (phen=1,10‐phenanthroline, dmp=2,9‐dimethyl‐1,10‐phenanthroline, dppzi=dipyrido[3,2‐a:2′,3′‐c]phenazine‐10,11‐imidazole) were prepared. Complex 1 can emit luminescence in the absence and presence of G‐quadruplexes DNA. However, with ?CH₃ substituent on the 2‐ and 9‐positions of the phen ancillary ligand, no detectable luminescence is observed for complex 2 in any organic solvent or in the absence and/or presence of G‐quadruplex DNA. Experimental and molecular docking studies indicated that both complexes interacted with the human telomeric repeat AG3(T2AG3)3 (22AG) G‐quadruplex with the stoichiometric ratio of 1:1, but the two complexes showed different G‐quadruplex DNA binding affinity. Complex 1 binds to the G‐quadruplexes DNA more tightly than complex 2 does. Our results demonstrate that methyl groups on the phen ancillary ligand significantly affect the spectral properties and the overall DNA binding behavior of the complexes. Such difference in spectral properties and DNA binding affinities of these two complexes can be reasonably explained by DFT/TD‐DFT calculations. This work provides guidance not only on exploring the G‐quadruplexes DNA binding behavior of complexes, but also understanding the unique luminescence mechanism.     

Synthesis,characterization, and DNA binding of ruthenium(II) complexes with 2-benzo[b] furan-2-yl-1H-imidazo[4,5f][1,10]phenanthroline as an intercalative ligand

DNA-binding properties of a number of ruthenium complexes with different polypyridine ligands are reported. The new polypyridine ligand BFIP (=2-benzo[b] furan-2-yl-1H-imidazo[4,5-f][1,10]phenanthroline) and its ruthenium complexes [Ru(bpy)₂BFIP]²⁺ (bpy = 2,2′-bipyridine), [Ru(dmb)₂BFIP]²⁺ (dmb = 4,4′-dimethyl-2,2′-bipyridine), and [Ru(phen)₂BFIP]²⁺ (phen = 1,10-phenanthroline) have been synthesized and characterized by elemental analysis, mass spectra, IR, UV-Vis, ¹H- and ¹³C-NMR, and cyclic voltammetry. The DNA binding of these complexes to calf-thymus DNA (CT-DNA) was investigated by spectrophotometric, fluorescence, and viscosity measurements. The results suggest that ruthenium(II) complexes bind to CT-DNA through intercalation. Photocleavage of pBR 322 DNA by these complexes was also studied, and [Ru(phen)₂BFIP]²⁺ was found to be a much better photocleavage agent than the other two complexes.     

Luminescent Ruthenium(II) Polypyridyl Complexes as Nonviral Carriers for DNA Delivery

Two new luminescent ruthenium(II) polypyridyl complexes, [Ru(bpy)₂(tpt‐phen)]Cl₂ ( 1 ; bpy=2,2′‐bipyridine, tpt‐phen=triptycenyl‐1,10‐phenanthroline) and [Ru(phen)₂(tpt‐phen)]Cl₂ ( 2 ; phen=1,10‐phenanthroline), have been developed as potential nonviral vectors for DNA delivery. Photophysical and electrochemical properties of the complexes have been investigated and corroborated with electronic structure calculations. DNA condensation by these complexes has been investigated by UV/Vis and emission spectroscopy, circular dichroism spectroscopy, atomic force microscopy, dynamic light scattering, confocal microscopy, and electrophoretic mobility studies. These complexes interact with DNA and efficiently condense DNA into globular nanoparticles that are taken up efficiently by HeLa cells. DNA cleavage inability and biocompatibility of complexes have been explored. Both complexes have good gene transfection abilities.     

Photoreaction of [Ru(hat)2phen]2+ with guanosine-5'-monophosphate and DNA: formation of new types of photoadducts

[Ru(hat)2phen]2+ (HAT=1,4,5,8,9,12-hexaazatriphenylene, phen=1,10-phenanthroline) interacts with a good affinity with polynucleotides and DNA by intercalation, despite the presence of a second voluminous ancillary HAT ligand. It photoreacts with guanosine-5'-monophosphate (GMP). From HPLC, ESMS and NMR analyses, it can be concluded that this complex forms photoadducts with GMP. In contrast to the photoadducts isolated with Ru-TAP complexes (TAP=1,4,5,8-tetraazaphenanthrene), the photoadducts with [Ru(hat)2phen]2+ contain a covalent link between the oxygen atom of the guanine unit and a HAT ligand. Formation of oxidised photoadducts and compounds resulting from the addition of two GMP entities to the complex are also detected as side products. In the presence of oligo- and polynucleotides, [Ru(hat)2phen]2+ yields photoadducts when guanine bases are present.     

Synthesis,characterization, and DNA-binding of [Co(phen)2(CPIA)]3+, [Co(phen)2(BIP)]3+, and [Co(phen)2(CIP)]3+

Three ligands, 2-(3-(carboxymethyl)-1,10-phenanthroline-[5,6-d]imidazole-1-yl)acetate (CPIA), 2-(benzo[d][1,3]dioxol-4-yl)-1H-imidazo[4,5-f][1,10]phenanthroline (BIP), and 2-(9H-carbazol-3-yl)-1H-imidazo[4,5-f][1,10]phenanthroline (CIP), and their complexes, [Co(phen)₂(CPIA)]³⁺ (1) (phen = 1,10-phenanthroline), [Co(phen)₂(BIP)]³⁺ (2), and [Co(phen)₂(CIP)]³⁺ (3), have been synthesized and characterized. Binding of the three complexes with calf thymus DNA (CT-DNA) has been investigated by spectroscopic methods, cyclic voltammetry, and viscosity measurements. The three complexes bind to DNA through an intercalative mode, and the size and shape of the intercalative ligands have significant effects on the binding affinity of complexes to CT-DNA.     

Targeting abasic sites and single base bulges in DNA with metalloinsertors

The site-specific recognition of abasic sites and single base bulges in duplex DNA by sterically expansive rhodium metalloinsertors has been investigated. Through DNA photocleavage experiments, Rh(bpy)2(chrysi)3+ is shown to bind both abasic sites and single base bulges site-specifically and, upon irradiation, to cleave the backbone of the defect-containing DNA. Photocleavage titrations reveal that the metal complex binds DNA containing an abasic site with high affinity (2.6(5) x 106 M-1), comparably to the metalloinsertor and a CC mismatch. The complex binds single base bulge sites with lower affinity (approximately 105 M-1). Analysis of cleavage products and the correlation of affinities with helix destabilization suggest that Rh(bpy)2(chrysi)3+ binds both lesions via metalloinsertion, as observed for Rh binding at mismatched sites, a binding mode in which the mismatched or unpaired bases are extruded from the helix and replaced in the base stack by the sterically expansive ligand of the metalloinsertor.     

新型多吡啶配体的设计及其对配合物与DNA作用机制的影响

近年来 ,以钌 ( )多吡啶配合物为探针研究 DNA的结构已成为生物无机化学领域中的一个热点[1,2 ] .这些配合物由于热力学稳定性好 ,光化学和光物理信息丰富 ,在研究 DNA内部的电子转移和Fig.1　 Structures of the ligandsDNA的结构识别等方面均有重要的作用[3～ 7] .在配合物与 DNA的相互作用中 ,配合物的形状、大小以及中心离子电荷等都有一定的影响[8] ,其中 ,配合物的形状起着至关重要的作用 ,与 DNA的形状匹配的配合物与DNA的结合较强 .这些配合物中通常含有平面性较大的芳香环配体 ,可插入到 DNA的碱基对之间 ,并与 DNA具有…